The only ones to show up in the series were the Energon Saber and the Star Saber. Technically there was also the Vorpal Saber used by the Nemesis Prime, but that was as much a part of him as it was an actual weapon.

The Star Saber was written as the most powerful. It was able to cleave through other Transformers, and its power was enough that it could make up for any lack of skill from the wielder (as seen in Scavenger's first appearance)

The Energon Saber was just treated as a group of Mini-cons who happened to form a sword, it did not seem to have the same special properties as the Star Saber.

Also, if you go by the comics, the Star Saber was directly linked to the power of the one that wielded it. If someone like Megatron used it, his strength could push them to new levels of power, but also corrupt them into the Dark Saber.

So by all accounts, the Star Saber is the most powerful of the bunch. Granted, we never got to see the Energon Saber in the comics or got a profile book entry for it - I'd imagine it would have been just as powerful, if not even more powerful.